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A young boy, Michael (Bill Milner) and his parents move into an decrepit old house to make room for the new baby that his mother (Kelly Macdonald) and father (John Simm) are expecting. The house is old and needs repair. Michael feels pushed out by his parents who are preoccupied with the state of the house and the new baby. Michael ventures out into the garden and finds an old shed. While looking around the gloomy and uninhabitable place he hears someone say "Who's there?" and runs. It later turns out that this is Skellig (Tim Roth). Michael's mother has been busy cleaning in the house when she goes into premature labour. Michael helps by calling an ambulance but blames himself for what has happened. The baby is premature and has to stay in hospital for some time. Eventually she comes home, apparently well.

Michael's mum wants to get rid of the old shed where Michael was exploring. Then the baby becomes sick once more and has to go back into hospital with a potentially fatal heart problem. Michael finds a girl called Mina (Skye Bennett) sitting on his wall and they become friends. While the baby is in hospital, the mum blames the dad for moving into the house. Michael's dad starts to drink and, late one night, goes to the shed and starts to thump it. He goes to look for matches; Michael gets Skellig out of the shed before it ignites. Michael places Skellig in the woods while he goes to Mina's house, where he shows her his burned hand. Michael and Mina take Skellig to what looks like a tall tower and this is when they see that Skellig has wings. They take care of Skellig and provide him with food. Mina and Michael hold hands with Skellig and fly mystically around in a circle. It is revealed that Skellig can perform magic as Michael's hand is cured.

Michael talks to Grace, an old lady whom he talks to every time he is at the hospital to visit with the new baby. He promises her that he will come the next day to see her. The next day when the baby goes in for the operation, he goes to visit Grace, but she has died in her sleep the night before. He runs to Skellig and tells him to cure the baby as he did his hand. To prove that he can heal his baby sister, Michael jumps off the tower, only to be caught by Skellig. Skellig tells him to fall asleep while flying and he does.

Skellig goes to the hospital and walks past everyone but no one sees him. Even Michael's mother doesn't notice when he walks into the baby's room. Skellig picks the baby out of her cot and does as before: flies off the ground and spins around as the baby lies sleeping in his arms. This miraculously cures the baby, much to the family's delight. When Michael asks the baby's name, they tell him that they can't find the right one, and he suggests Grace. Baby Grace and her family go back to the house where her room is bright yellow; dad had been working on it while she was in hospital. (In the novel, the baby is named Joy, after a poem by William Blake.)

At the end, Skellig is at the tower with Michael and Mina, who ask him what he's going to do now, and leave him with a parting gift, a bottle of nectar ale. Skellig answers that he is going "somewhere."